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Transparency available again
[jalview.git]
/
src
/
jalview
/
schemes
/
UserColourScheme.java
diff --git
a/src/jalview/schemes/UserColourScheme.java
b/src/jalview/schemes/UserColourScheme.java
index
95e9a32
..
3349283
100755
(executable)
--- a/
src/jalview/schemes/UserColourScheme.java
+++ b/
src/jalview/schemes/UserColourScheme.java
@@
-134,7
+134,7
@@
public class UserColourScheme
{
\r
StringTokenizer st = new StringTokenizer(paramValue, ";");
\r
StringTokenizer st2;
\r
{
\r
StringTokenizer st = new StringTokenizer(paramValue, ";");
\r
StringTokenizer st2;
\r
- String token=null, colour, residues, residue;
\r
+ String token=null, colour, residues;
\r
try{
\r
while (st.hasMoreElements())
\r
{
\r
try{
\r
while (st.hasMoreElements())
\r
{
\r
@@
-146,6
+146,12
@@
public class UserColourScheme
while (st2.hasMoreTokens())
\r
{
\r
token = st2.nextToken();
\r
while (st2.hasMoreTokens())
\r
{
\r
token = st2.nextToken();
\r
+
\r
+ if (ResidueProperties.aaIndex[token.charAt(0)]==-1)
\r
+ continue;
\r
+
\r
+ int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
\r
+
\r
if(token.equalsIgnoreCase("lowerCase"))
\r
{
\r
if (lowerCaseColours == null)
\r
if(token.equalsIgnoreCase("lowerCase"))
\r
{
\r
if (lowerCaseColours == null)
\r
@@
-157,10
+163,6
@@
public class UserColourScheme
continue;
\r
}
\r
\r
continue;
\r
}
\r
\r
- int colIndex =
\r
- ( (Integer) ResidueProperties.aaHash.
\r
- get(token)).intValue();
\r
-
\r
if(token.equals(token.toLowerCase()))
\r
{
\r
if(lowerCaseColours==null)
\r
if(token.equals(token.toLowerCase()))
\r
{
\r
if(lowerCaseColours==null)
\r
@@
-186,7
+188,7
@@
public class UserColourScheme
\r
public Color findColour(String s, int j)
\r
{
\r
\r
public Color findColour(String s, int j)
\r
{
\r
- int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
\r
+ int index = ResidueProperties.aaIndex[s.charAt(0)];
\r
\r
if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
\r
{
\r
\r
if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
\r
{
\r